October 18, 2010
Bioconductors:
We are pleased to announce Bioconductor 2.7, consisting of 419 software packages. There are 34 new packages, and many updates and improvements to existing packages. Bioconductor 2.7 is compatible with R 2.12.0, and is supported on Linux, 32- and 64-bit Windows, and Mac OS. Visit
for details and downloads.
Contents
- Getting Started with Bioconductor 2.7
- New Software Packages
- Web Site Updates
Getting Started with Bioconductor 2.7
To install Bioconductor 2.7:
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Install R 2.12.0. Bioconductor 2.7 has been designed expressly for this version of R.
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Follow the instructions here:
http://bioconductor.org/install/
Please visit http://bioconductor.org for details and downloads.
New Software Packages
There are 34 new packages in this release of Bioconductor.
ADaCGH2
Analysis of aCGH experiments using parallel computing and ff objects
attract
Methods to find gene expression modules representing drivers in Kauffman’s Attractor Landscape
BHC
Bayesian Hierarchical Clustering
BioNet
Functional analysis of biological networks
CGEN
Case-control studies in genetic epidemiology
CoGAPS
Coordinated Gene Activity in Pattern Sets
coRNAi
Analysis of co-knock-down RNAi data
CRImage
Classify cells and calculate tumor cellularity
DEgraph
Two-sample tests on a graph
fabia
Factor Analysis for Bicluster Acquisition
farms
Factor Analysis for Robust Microarray Summarization
gage
Generally Applicable Gene-set Enrichment for Pathway Analysis
GeneGA
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
HTSanalyzeR
Network and gene set enrichment analysis pipeline for high throughput screens.
imageHTS
Analysis of high-throughput microscopy-based screens
iSeq
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
IsoGeneGUI
A graphical user interface to dose-response analysis of microarray data
les
Identifying Loci of Enhanced Significance in Tiling Microarray Data
LVSmiRNA
LVS normalization for Agilent miRNA data
MBCB
Model-based Background Correction for Beadarray
MEDIPS
MeDIP-Seq data analysis
Mulcom
Differential expression and false discovery rate calculation through multiple comparison
netresponse
Functional network analysis
NTW
Predict gene network using an Ordinary Differential Equation (ODE) based method
NuPoP
Nucleosome positioning prediction
ontoCAT
Ontology parsing
OTUbase
Deals with OTU data
PatientGeneSets
Patient-oriented gene-set analysis
R453Plus1Toolbox
Import and analyze data from Roche’s Genome Sequencer System.
RCytoscape
Display and manipulate graphs in Cytoscape
RDRToolbox
Nonlinear dimension reduction with Isomap and LLE.
RMAPPER
Interface to the MAPPER database of transcription factor binding sites
rnaSeqMap
rnaSeq analyses using xmapcore database
SQUADD
Add-on to Standardized Qualitative Dynamical Systems software for the logical models approach to analysis of complex dynamic systems
Web Site Updates
The Bioconductor web site underwent significant changes during the last release cycle. The web site includes extensive help resources for both users and package developers, in addition to information on package installation. One particularly useful feature in navigating the large numbers of available packages is the updated biocViews widget